RNA-Seq Analysis Reveals an Essential Role of the cGMP-PKG-MAPK Pathways in Retinal Degeneration Caused by Cep250 Deficiency

Abstract

Usher syndrome (USH) is characterised by degenerative vision loss known as retinitis pigmentosa (RP), sensorineural hearing loss, and vestibular dysfunction. RP can cause degeneration and the loss of rod and cone photoreceptors, leading to structural and functional changes in the retina. Cep250 is a candidate gene for atypical Usher syndrome, and this study describes the development of a Cep250 KO mouse model to investigate its pathogenesis. OCT and ERG were applied in Cep250 and WT mice at P90 and P180 to access the general structure and function of the retina. After recording the ERG responses and OCT images at P90 and P180, the cone and rod photoreceptors were visualised using an immunofluorescent stain. TUNEL assays were applied to observe the apoptosis in Cep250 and WT mice retinas. The total RNA was extracted from the retinas and executed for RNA sequencing at P90. Compared with WT mice, the thickness of the ONL, IS/OS, and whole retina of Cep250 mice was significantly reduced. The a-wave and b-wave amplitude of Cep250 mice in scotopic and photopic ERG were lower, especially the a-wave. According to the immunostaining and TUNEL stain results, the photoreceptors in the Cep250 retinas were also reduced. An RNA-seq analysis showed that 149 genes were upregulated and another 149 genes were downregulated in Cep250 KO retinas compared with WT mice retinas. A KEGG enrichment analysis indicated that cGMP-PKG signalling pathways, MAPK signalling pathways, edn2-fgf2 axis pathways, and thyroid hormone synthesis were upregulated, whereas protein processing in the endoplasmic reticulum was downregulated in Cep250 KO eyes. Cep250 KO mice experience a late-stage retinal degeneration that manifests as the atypical USH phenotype. The dysregulation of the cGMP-PKG-MAPK pathways may contribute to the pathogenesis of cilia-related retinal degeneration.

Keywords: Cep250-KO mice; RNA sequencing; Usher syndrome; cGMP-PKG-MAPK signalling pathways; retinal degeneration.

Figure 1

Thickness of different retinal layers of Cep250 and WT mice taken by performing spectral-domain optical coherence tomography (SD−OCT) of Cep250 and WT mice. (A) Representative OCT images and thickness of the whole retina of Cep250 and WT mice at P180. (B–D) Measurement of the thickness of the ONL, IS/OS, and whole retina at P90. (E–G) Measurement of the thickness of the ONL, IS/OS, and whole retina at P180. The values are presented as the means ± SEMs. * p < 0.05, ** p < 0.01, *** p < 0.001 (Student’s t-test). n: the number of animals used for statistical analysis.

Figure 2

Retinal function of Cep250 and WT mice at P90 as determined by the ERG. (A) Representative waves under dark 3.0, dark 10.0, and light 3.0 conditions. (B–E) Statistical analysis of a-wave and b-wave amplitudes at P90. Means ± SEMs. * p < 0.05; ns = no significance; n: the number of animals used for statistical analysis. Student’s t-test.

Figure 3

Immunostaining of photoreceptors and TUNEL staining of retinas. (A) Immunostaining of rhodopsin of Cep250 and WT mice at P180 (magnification: 200×). (B,C) Immunostaining of S-opsin and M-opsin of Cep250 and WT mice at P180 (magnification: 200×). (D) TUNEL staining of Cep250 and WT mice at P180 (magnification: 200×). (E) Corresponding quantitative data of the relative expression in (A–D). The values are presented as the means ± SEMs. * p < 0.05. Student’s t-test. n = 3.

Figure 4

Transcriptional profiling of retinas from Cep250 KO mice and verification of gene expression. (A) Volcano plot showing highlights of DEGs from Cep250 KO retinas compared with WT retina. (B) The significantly enriched pathways in the Cep250 KO retina (compared with WT retina) from the KEGG analysis of the DEGs. (C) Bar figures showing the relative gene expression measured by the qPCR analysis. Means ± SEMs. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001. Student’s t-test. n = 3.